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At least 343 records · Page 19Linked to original sources
PubMed1996

A protein class database organized with ProSite protein groups and PIR superfamilies.

A protein class (ProClass) database is developed as a "value-added" "second-generation" database organized according to family relationships. The database collects non-redundant protein sequence entries from SwissProt and PIR databases, and classifies them in families defined collectively by the ProSite protein groups and PIR superfamilies. The major objectives of the database are to maximize family information retrieval, to provide speedy family identification, and to help organizing existing protein sequence databases. The database has two sub-databases: PCFam (ProClass Family) to define protein families and provide links to ProSite patterns and PIR superfamilies, and PCSeq (ProClass Sequence) to describe sequence entries and provide links to PCFam, SwissProt, PIR, and ProSite databases. The current ProClass release has a total of 85,165 sequence entries, about half of which are classified in 3072 ProClass families; it also contains 10,431 newly established SwissProt-PIR links. The database can help reveal domain structures of related families, define new ProSite and PIR families, and provide family assignments for unclassified sequence entries. New ProSite and PIR family members are readily identified via database cross-reference, including 9437 SwissProt entries and 8522 PIR entries. False negative family members missed by both ProSite and PIR are detected using a neural network family identification system. The newly identified superfamily memberships are being incorporated into the current PIR database releases in a collaborative effort with the PIR. The ProClass database is accessible through anonymous FTP and on-line search on the World Wide Web.

Amino Acid Sequence↗
PubMedDate not supplied

Using Raman spectroscopy to solve crime: inks, questioned documents and fraud.

Raman microscopy is becoming a tool of major importance in forensic analysis, particularly of drugs and explosives. It is a non-invasive, non-destructive chemical probe allowing samples to be examined in their entirety without any preparation. This paper demonstrates the use of the technique as a general tool for inks analysis. Furthermore, it addresses two important issues that historically have been extremely difficult for the professional document examiner, namely, comparison of black ballpoint inks and the chronological sequencing of crossed ink lines. We show that Raman can successfully distinguish between a representative sample of commercially available black ballpoint inks. This data has been converted into a database for future reference. A method for chronological sequencing of crossed ink lines has been developed using confocal Raman microscopy. Case study work has shown the feasibility of this approach.

Databases, Factual↗
PubMed1994

Implementation of a relational patient record with integration of educational and reference information.

The clinician must identify pertinent diagnostic information and develop appropriate medical management plans in the context of rapidly changing research information, new therapeutic options and expanding diagnostic modalities. To assist in recognition of patterns relevant to diagnostic or therapeutic interventions, the medical record must be presented in a format that emphasizes important data interrelationships. Reference and educational information specifically pertinent to the case being reviewed must be immediately accessible. A system that presents point of care patient centered clinical information, a summarized patient record, in a relational format with linked reference information has been developed. Data is acquired from the VA patient information database and provided over a PC network. At the time of data transfer, preliminary analysis and reorganization of data is performed such that interrelationships between laboratory, pharmacy and diagnostic information can be rapidly recognized. During data compilation reference and educational information is linked with patient data such that it can be accessed with a mouse click ("hotspot") when the record is subsequently reviewed. The medical record and CD-ROM based reference databases are then made available to users on a PC network in a Windows (tm) environment. Initial experience with the system is very favorable and suggests that evaluation of patient data may be significantly enhanced.

Computer Communication Networks↗
PubMed1998

PAH Mutation Analysis Consortium Database: 1997. Prototype for relational locus-specific mutation databases.

PAHdb (http://www.mcgill.ca/pahdb ) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897). Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without apparent effect on phenotype. PAHdb modules contain mutations, polymorphic haplotypes, genotype-phenotype correlations, expression analysis, sources of information and the reference sequence; the database also contains pages of clinical information and data on three ENU mouse orthologues of human HPA. Only six different mutations account for 60% of human HPA chromosomes worldwide, mutations stratify by population and geographic region, and the Oriental and Caucasian mutation sets are different (Fig. 3). PAHdb provides curated electronic publication and one third of its incoming reports are direct submissions. Each different mutation receives a systematic (nucleotide) name and a unique identifier (UID). Data are accessed both by a Newsletter and a search engine on the website; integrity of the database is ensured by keeping the curated template offline. There have been >6500 online interrogations of the website.

Animals↗
PubMed1998

A database of germline p53 mutations in cancer-prone families.

We created a comprehensive database covering all published cases of germline p53 mutations. The current version lists 580 tumours in 448 individuals belonging to 122 independent pedigrees. The database describes each p53 mutation (type of the mutation, exon and codon affected by the mutation, nucleotide and amino acid change), each family (family history of cancer, diagnosis of Li-Fraumeni syndrome), each affected individual (sex, generation, p53 status, from which parent the mutation was inherited) and each tumour (type, age of onset, p53 status-loss of heterozygosity, immunostaining). Each entry contains the original reference(s). The database is freely available and can be obtained from http://www.lf2.cuni.cz

Computer Communication Networks↗
PubMed1997

UnCover on the Web: search hints and applications in library environments.

Among the huge maze of resources available on the Internet, UnCoverWeb stands out as a valuable tool for medical libraries. This up-to-date, free-access, multidisciplinary database of periodical references is searched through an easy-to-learn graphical user interface that is a welcome improvement over the telnet version. This article reviews the basic and advanced search techniques for UnCoverWeb, as well as providing information on the document delivery functions and table of contents alerting service called Reveal. UnCover's currency is evaluated and compared with other current awareness resources. System deficiencies are discussed, with the conclusion that although UnCoverWeb lacks the sophisticated features of many commercial database search services, it is nonetheless a useful addition to the repertoire of information sources available in a library.

Computer Communication Networks↗
PubMed1997

Lifelong self-directed learning using a computer database of clinical questions.

Physicians often have self-perceived knowledge gaps when they are seeing patients. Traditional continuing medical education is designed to meet the knowledge gaps of groups rather than individual physicians with specific patient problems. Physicians with clinical information needs are advised to critically evaluate high-quality original research in order to practice "evidence-based medicine." But this advice may be unrealistic for busy clinicians. We propose a system for documenting self-perceived information needs using a computer database. Concise answers to these needs are included in the database along with reference citations supporting the answers. The system tracks continuing education efforts, directs patient care decisions, and focuses lifelong learning on relevant topics. We emphasize the importance of being sensitive to personal information needs and the benefits of maintaining a record of these needs.

Clinical Medicine↗
PubMed1999

Analysis of flanking sequences from dissociation insertion lines: a database for reverse genetics in Arabidopsis.

We have generated Dissociation (Ds) element insertions throughout the Arabidopsis genome as a means of random mutagenesis. Here, we present the molecular analysis of genomic sequences that flank the Ds insertions of 931 independent transposant lines. Flanking sequences from 511 lines proved to be identical or homologous to DNA or protein sequences in public databases, and disruptions within known or putative genes were indicated for 354 lines. Because a significant portion (45%) of the insertions occurred within sequences defined by GenBank BAC and P1 clones, we were able to assess the distribution of Ds insertions throughout the genome. We discovered a significant preference for Ds transposition to the regions adjacent to nucleolus organizer regions on chromosomes 2 and 4. Otherwise, the mapped insertions appeared to be evenly dispersed throughout the genome. For any given gene, insertions preferentially occurred at the 5' end, although disruption was clearly possible at any intragenic position. The insertion sites of >500 lines that could be characterized by reference to public databases are presented in a tabular format at http://www.plantcell. org/cgi/content/full/11/12/2263/DC1. This database should be of value to researchers using reverse genetics approaches to determine gene function.

Arabidopsis↗
PubMed1993

Matching references with MEDLINE via TCP/IP.

Bibliographic references are an important part of databases and information resources used by clinicians and biomedical researchers. In addition to the obvious clerical advantages of standard references, bibliographic references can also be used as links to related items in different data sets. This paper describes an effort that involved matching references from a variety of disparate databases to canonical MEDLINE references. The references matched were those involved in a database unification project which is part of the Mouse Genome Informatics effort at The Jackson Laboratory. Software was developed to take advantage of a commercially available retrieval engine which accesses MEDLINE on CD-ROM disks. The software permits client programs on UNIX/C, and potentially other environments, to access unabridged MEDLINE via networks supporting the TCP/IP protocols. The matching process described can be used as a model for similar efforts with different research or clinical data sets, as well as different hardware or software environments.

Animals↗
PubMed2026

GRNContext: an interactive web platform for contextualized gene regulatory networks visualization across human cancers.

SUMMARY: While current Gene Regulatory Network (GRN) databases provide comprehensive reference maps of potential interactions between transcription factors and target genes, they do not specify which regulatory interactions are active within specific biological contexts. This limitation is particularly critical in cancer, where transcriptional programs are inherently tissue-specific. To address this gap, we developed GRNContext, an interactive web platform designed for the visualization, exploration, and comparative analysis of gene regulatory networks contextualized across 33 cancer types from The Cancer Genome Atlas (TCGA). Our approach uses the TFLink human reference GRN as a starting point and integrates TCGA transcriptomic profiles to infer cancer-specific regulatory activity. Regulatory relevance was assessed using complementary machine learning and statistical methods, which were unified into a consensus score to prioritize and filter the most relevant candidate regulators for each target gene. By providing both curated context-specific GRNs and a user-friendly platform, GRNContext constitutes a comprehensive and accessible resource that supports mechanistic investigations, hypothesis generation, and translational research focused on transcriptional regulation in cancer. AVAILABILITY AND IMPLEMENTATION: GRNContext is supported by all major browsers and freely available on the web at https://apps.cienciavida.org/grncontext. It is implemented as a client-server web application featuring a FastAPI backend and a React frontend utilizing Cytoscape.js for interactive network visualization, all containerized via Docker for cross-platform compatibility.

Humans↗
PubMed2000

Do mucosal defensive agents improve the cure rate when used with dual or triple therapy regimens for eradicating Helicobacter pylori infection?

BACKGROUND: Some of mucosal defensive agents have anti-Helicobacter pylori activities. However, their effectiveness in eradicating H. pylori infection has not been evaluated. AIM: To assess the additive effect of mucosal defensive agents in eradication regimens using statistical analysis. METHODS: Pertinent studies were retrieved using the Medline and the Igaku-chuo-zasshi databases in Japan, reference and congress abstract lists. Studies in which regimens consisted of dual or triple therapy with mucosal defensive agents and without them, were selected from the retrieved studies. Eradication rates were extracted from studies according to intention-to-treat analysis. We evaluated the efficacies of mucosal defensive agents by pooled relative risk of eradication rates and its 95% confidence intervals (95% CI), which were calculated by Mantel-Haenszel method. Heterogeneity among the studies in treatment effect was evaluated by a chi2-test. RESULTS: In dual therapy regimens, mucosal defensive agents demonstrated significant additive effects (pooled relative risk 1.41; 95% CI: 1.24-1.61). In triple therapy regimens, these agents did not provide significant additive effect. The clinical usefulness of specific agents could not be established, when each agent was analysed independently. CONCLUSIONS: Mucosal defensive agents improve the cure rate when used with existing dual therapy regimens for eradicating H. pylori infection.

Anti-Ulcer Agents↗
PubMed1996

Implementation of a reference management system, MacRefer, under HyperCard.

We have developed a reference management system, MacRefer, using HyperTalk on Macintosh personal computers. Using this program, one can automatically acquire data from databases created by EndNote Plus and from OVID- or Medlar-formatted records downloaded via an online use of Medline. The MacRefer's capability of formatting bibliographic database in user-defined formats is comparable with the exemplified bibliography maker, EndNote Plus. Moreover, MacRefer has several competitive features, which are insufficiently equipped with EndNote Plus. For example, MacRefer is capable of (1) maintaining subsets within a database, (2) executing complex, structured searches combining up to nine keywords for any data field with the results and search conditions preserved, and (3) easily browsing (a portion of) reference database. Although MacRefer cannot be recognized as an absolute alternative of EndNote Plus because of several limitations inherent to HyperCard, the compensatory use of these two programs will expand the personal utilization of bibliographic databases.

Computers↗
PubMed2000

Depression and poor glycemic control: a meta-analytic review of the literature.

OBJECTIVE: Depression is common among patients with diabetes, but its relationship to glycemic control has not been systematically reviewed. Our objective was to determine whether depression is associated with poor glycemic control. RESEARCH DESIGN AND METHODS: Medline and PsycINFO databases and published reference lists were used to identify studies that measured the association of depression with glycemic control. Meta-analytic procedures were used to convert the findings to a common metric, calculate effect sizes (ESs), and statistically analyze the collective data. RESULTS: A total of 24 studies satisfied the inclusion and exclusion criteria for the meta-analysis. Depression was significantly associated with hyperglycemia (Z = 5.4, P < 0.0001). The standardized ES was in the small-to-moderate range (0.17) and was consistent, as the 95% CI was narrow (0.13-0.21). The ES was similar in studies of either type 1 or type 2 diabetes (ES 0.19 vs. 0.16) and larger when standardized interviews and diagnostic criteria rather than self-report questionnaires were used to assess depression (ES 0.28 vs. 0.15). CONCLUSIONS: Depression is associated with hyperglycemia in patients with type 1 or type 2 diabetes. Additional studies are needed to establish the directional nature of this relationship and to determine the effects of depression treatment on glycemic control and the long-term course of diabetes.

Adult↗
PubMed2000

Evidence-based medicine in nephrology: identifying and critically appraising the literature.

BACKGROUND: Uncertainties about best management of end-stage renal disease (ESRD) are reflected in wide variations in practice. Systematic reviews aim to reduce uncertainty by strengthening the evidence base for clinical practice, allowing estimation of the benefits and risks of particular interventions, whilst minimizing the potential for bias. This paper describes the methods and conduct of six systematic reviews of aspects of the management of ESRD, and the yield in terms of trials found. METHODS: Our methodology was based on that recommended by the Cochrane Collaboration (an international initiative set up to perform and disseminate systematic reviews of health care). It involved a systematic search of electronic databases and bibliographic reference lists, together with handsearching of Kidney International for studies relevant to the management of ESRD, followed by a systematic assessment of study quality. RESULTS: Around 12,000 abstracts were assessed which had been identified from electronic sources. Of these, 2085 (18%) were deemed to be reports of possible randomized or quasi-randomized controlled trials relevant to the management of ESRD. Three hundred and forty were relevant to the six specific reviews, and after assessment of the full manuscripts, 39 studies were finally included in our reviews. Reports of a further nine trials, which were identified from other sources, were also included. The broad search adopted allowed the parallel development of a register of trials of all aspects of the management of ESRD. CONCLUSIONS: This study has demonstrated that the methodology of systematic reviews, as promoted by the Cochrane Renal Group, is feasible but has significant resource implications. The development of a register of randomized controlled trials (RCTs) related to the management of ESRD will facilitate this form of research in the future.

Databases as Topic↗
PubMed2000

Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome.

OBJECTIVES: Irritable bowel syndrome is the most common gastrointestinal diagnosis. The symptoms of irritable bowel syndrome are similar to those of small intestinal bacterial overgrowth. The purpose of this study was to test whether overgrowth is associated with irritable bowel syndrome and whether treatment of overgrowth reduces their intestinal complaints. METHODS: Two hundred two subjects in a prospective database of subjects referred from the community undergoing a lactulose hydrogen breath test for assessment of overgrowth were Rome I criteria positive for irritable bowel syndrome. They were treated with open label antibiotics after positive breath test. Subjects returning for follow-up breath test to confirm eradication of overgrowth were also assessed. Subjects with inflammatory bowel disease, abdominal surgery, or subjects demonstrating rapid transit were excluded. Baseline and after treatment symptoms were rated on visual analog scales for bloating, diarrhea, abdominal pain, defecation relief, mucous, sensation of incomplete evacuation, straining, and urgency. Subjects were blinded to their breath test results until completion of the questionnaire. RESULTS: Of 202 irritable bowel syndrome patients, 157 (78%) had overgrowth. Of these, 47 had follow-up testing. Twenty-five of 47 follow-up subjects had eradication of small intestinal bacterial overgrowth. Comparison of those that eradicated to those that failed to eradicate revealed an improvement in irritable bowel syndrome symptoms with diarrhea and abdominal pain being statistically significant after Bonferroni correction (p < 0.05). Furthermore, 48% of eradicated subjects no longer met Rome criteria (chi2 = 12.0, p < 0.001). No difference was seen if eradication was not successful. CONCLUSIONS: Small intestinal bacterial overgrowth is associated with irritable bowel syndrome. Eradication of the overgrowth eliminates irritable bowel syndrome by study criteria in 48% of subjects.

Adult↗
PubMed2001

STRBase: a short tandem repeat DNA database for the human identity testing community.

The National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl.nist.gov/biotech/++ +strbase/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes.

Databases, Factual↗
PubMed2026

Management of Soft Tissue and Visceral Leiomyosarcomas.

IMPORTANCE: Leiomyosarcoma is a rare and heterogeneous malignant mesenchymal neoplasm associated with substantial morbidity and mortality. Given recent advances in biologic understanding and the complexity of leiomyosarcoma, a consensus-driven approach is needed to harmonize management and address remaining clinical and research gaps. OBJECTIVE: To provide an evidence-based synthesis of current diagnostic and therapeutic approaches for leiomyosarcoma by an international panel of physicians, researchers, and patient advocates, focusing on site-specific management, systemic therapy strategies, and key areas of clinical uncertainty, while identifying unmet needs and research priorities. EVIDENCE REVIEW: This review is based on a comprehensive evaluation of the literature, including clinical trials, observational studies, and international consensus guidelines. Sources were identified through MEDLINE (via PubMed) and Embase database searches and reference screening, then supplemented by multidisciplinary expert consensus. Emphasis was placed on studies informing diagnosis, surgical management, radiotherapy, and systemic therapy in leiomyosarcoma. FINDINGS: The rarity and heterogeneity of leiomyosarcoma poses substantial challenges in its management. In localized disease, complete surgical resection remains the cornerstone of treatment, with evidence supporting the use of site-specific perioperative treatment strategies. Prospective data supporting neoadjuvant or adjuvant chemotherapy are lacking, and the role of radiotherapy differs across anatomic disease sites and institutions. In advanced disease, multiple systemic therapies demonstrate activity, including anthracycline-based and gemcitabine-based combinations, trabectedin, and tyrosine kinase inhibitors, although optimal sequencing after first-line therapy remains undefined. Emerging data suggest potential benefit from treatment continuation strategies and selected use of local therapies in oligometastatic settings. Molecular heterogeneity is increasingly recognized but has not yet translated into routine clinical implementation, and integration of molecular profiling into diagnostic pathways for predictive and therapeutic insights remains an unmet need. CONCLUSIONS AND RELEVANCE: This international consensus addresses the diagnosis and management of leiomyosarcoma. Management requires a multidisciplinary, site-specific approach informed by limited but evolving evidence. Key uncertainties persist, particularly regarding perioperative therapy, optimal sequencing and combination of systemic treatments, and integration of molecular data. Continued international collaboration and leiomyosarcoma-specific clinical trials are needed to refine treatment strategies and improve patient outcomes.

Journal Article↗
PubMed2000

Serum protein immunogenicity: implications for liver xenografting.

The objectives of this study were threefold: (i) assess immunogenicity of donor plasma proteins following hepatic xenotransplantation, (ii) identify potential immunogens, and (iii) consider the implications of antibody formation against these plasma proteins in xenograft survival. We studied liver and heart xenografts in a concordant combination, hamster to rat. All grafts were examined at necropsy for evidence of rat immunoglobulin G (IgG) deposition. Cardiac xenografts were placed in recipients who had, or had not, been sensitized with hamster serum. Hepatic xenografts were placed in naive recipients to see if antibodies to hamster serum proteins could be eluted from the rejecting organ. Sera of immunized rats were examined for the presence of anti-hamster antibodies by immunoelectrophoresis and by Western blotting following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation of hamster serum. Antibodies in sera of immunized rats were compared with those eluted from rejecting livers. Candidate antigens were identified by tandem mass spectrometry, sequence analysis, and reference to protein databases. Results showed that sera of immunized rats recognized a minimum of four different antigens in hamster serum by immunoelectrophoresis, and a minimum of seven by the more sensitive SDS-PAGE Western blot. IgG eluted from rejecting livers bound three of seven candidate antigens recognized by sera of the immunized animals. Sequence analysis searches revealed proteinase inhibitors in each of the three SDS-PAGE bands common to the above samples. All of these candidate proteinase inhibitor immunogens share a common catabolic fate, uptake via the lipoprotein-related protein (LRP/alpha 2-macroglobulin receptor (CD91). Sensitization to hamster serum proteins hastened cardiac xenograft rejection in 30-50% of recipients (depending on sensitization protocol). Vascular deposition of rat IgG occurred in all rejecting xenografts. Antibody binding to proteinase inhibitors could disturb their functional activity and contribute to the pathogenesis of delayed xenograft rejection.

Amino Acid Sequence↗